Immunohistochemical (IHC) assays performed on formalin-fixed paraffin-embedded (FFPE) tissue sections traditionally have been semi-quantified by pathologist visual scoring of staining. IHC is useful for validating biomarkers discovered through genomics methods as large clinical repositories of FFPE specimens support the construction of tissue microarrays (TMAs) for high throughput studies. Due to the ubiquitous availability of IHC techniques in clinical laboratories, validated IHC biomarkers may be translated readily into clinical use. However, the method of pathologist semi-quantification is costly, inherently subjective, and produces ordinal rather than continuous variable data. Computer-aided analysis of digitized whole slide images may overcome these limitations. Using TMAs representing 215 ovarian serous carcinoma specimens stained for S100A1, we assessed the degree to which data obtained using computer-aided methods correlated with data obtained by pathologist visual scoring. To evaluate computer-aided image classification, IHC staining within pathologist annotated and software-classified areas of carcinoma were compared for each case. Two metrics for IHC staining were used: the percentage of carcinoma with S100A1 staining (%Pos), and the product of the staining intensity (optical density [OD] of staining) multiplied by the percentage of carcinoma with S100A1 staining (OD*%Pos). A comparison of the IHC staining data obtained from manual annotations and software-derived annotations showed strong agreement, indicating that software efficiently classifies carcinomatous areas within IHC slide images. Comparisons of IHC intensity data derived using pixel analysis software versus pathologist visual scoring demonstrated high Spearman correlations of 0.88 for %Pos (p < 0.0001) and 0.90 for OD*%Pos (p < 0.0001). This study demonstrated that computer-aided methods to classify image areas of interest (e.g., carcinomatous areas of tissue specimens) and quantify IHC staining intensity within those areas can produce highly similar data to visual evaluation by a pathologist. Virtual slides The virtual slide(s) for this article can be found here: http://www.diagnosticpathology.diagnomx.eu/vs/1649068103671302

Abstract:Immunohistochemical (IHC) assays performed on formalinfixed paraffinembedded (FFPE) tissue sections traditionally have been semiquantified by pathologist visual scoring of staining. IHC is useful for validating biomarkers discovered through genomics methods as large clinical repositories of FFPE specimens support the construction of tissue microarrays (TMAs) for high throughput studies. Due to the ubiquitous availability of IHC techniques in clinical laboratories, validated IHC biomarkers may be translated readily into clinical use. However, the method of pathologist semiquantification is costly, inherently subjective, and produces ordinal rather than continuous variable data. Computeraided analysis of digitized whole slide images may overcome these limitations. Using TMAs representing 215 ovarian serous carcinoma specimens stained for S100A1, we assessed the degree to which data obtained using computeraided methods correlated with data obtained by pathologist visual scoring. To evaluate computeraided image classification, IHC staining within pathologist annotated and softwareclassified areas of carcinoma were compared for each case. Two metrics for IHC staining were used: the percentage of carcinoma with S100A1 staining (%Pos), and the product of the staining intensity (optical density [OD] of staining) multiplied by the percentage of carcinoma with S100A1 staining (OD*%Pos). A comparison of the IHC staining data obtained from manual annotations and softwarederived annotations showed strong agreement, indicating that software efficiently classifies carcinomatous areas within IHC slide images. Comparisons of IHC intensity data derived using pixel analysis software versus pathologist visual scoring demonstrated high Spearman correlations of 0.88 for %Pos (p<0.0001) and 0.90 for OD*%Pos (p<0.0001). This study demonstrated that computeraided methods to classify image areas of interest (e.g., carcinomatous areas of tissue specimens) and quantify IHC staining intensity within those areas can produce highly similar data to visual evaluation by a pathologist. Virtual slides:The virtual slide(s) for this article can be found here: http://www.diagnosticpathology.diagnomx.eu/ vs/1649068103671302. Keywords:Annotation, Color deconvolution, Digital pathology, Immunohistochemistry, Intensity, Quantification, Software

* Correspondence: schme004@umn.edu 1 Department of Laboratory Medicine and Pathology, University of Minnesota, 420 Delaware Street SE, MMC76, Minneapolis, MN 55455, USA 3 BioNet, University of Minnesota, Minneapolis, MN, USA Full list of author information is available at the end of the article

studies to validate initial results of genomics studies often are lacking [5] or fail to confirm initial discoveryphase results [6], limiting clinical implementation of new disease biomarkers. Immunohistochemistry (IHC) is an important tech nique for biomarker validation for several reasons. First, it allows direct visualization of biomarker expression in his tologically relevant regions of the examined tissue. This is an important advantage over“grind and bind”assays in which tissue is solubilized for biochemical analysis, which may lead to false negative results if few biomarkerpositive